matterviz 0.4.0 → 0.4.1

package/dist/symmetry/symmetry-elements.js

@@ -0,0 +1,521 @@
+import * as math from '../math';
+// All element kinds in display order (axes first, then planes, then point elements).
+// Single source of truth for ordering — both the controls legend and the element list
+// returned by symmetry_elements_from_ops follow this sequence.
+export const SYM_ELEM_KINDS = [
+    `rotation`,
+    `screw`,
+    `rotoinversion`,
+    `mirror`,
+    `glide`,
+    `inversion`,
+];
+// Default overlay visibility: a SINGLE kind (proper rotation axes). High-symmetry
+// structures easily have 100+ distinct elements which, drawn all at once, bury the
+// structure entirely. Users opt into additional kinds individually via
+// SymmetryElementControls (or the show_kinds prop).
+export const DEFAULT_SHOW_SYM_KINDS = { rotation: true };
+// Human-readable labels + representative legend colors per kind. mirror/glide/
+// rotoinversion/inversion match the SymmetryElements.svelte render colors exactly;
+// rotation/screw axes are colored by rotation order in-scene, so their swatch uses the
+// 2-fold color as representative.
+export const SYM_ELEM_KIND_INFO = {
+    rotation: { label: `rotation axes`, color: `#e63946` },
+    screw: { label: `screw axes`, color: `#e76f51` },
+    mirror: { label: `mirror planes`, color: `#ffb703` },
+    glide: { label: `glide planes`, color: `#8ecae6` },
+    rotoinversion: { label: `rotoinversion axes`, color: `#9c27b0` },
+    inversion: { label: `inversion centers`, color: `#555555` },
+};
+// Tally elements per kind (for legend labels like "mirror planes (9)")
+export function count_symmetry_elements(elements) {
+    const counts = {};
+    for (const elem of elements)
+        counts[elem.kind] = (counts[elem.kind] ?? 0) + 1;
+    return counts;
+}
+// Whether the overlay would actually draw something: at least one PRESENT element whose
+// kind is ENABLED in show_kinds. Used to gate declutter so callers don't hide polyhedra /
+// shrink atoms when the enabled kinds match no present element (e.g. the rotation-only
+// default on an inversion-only P-1 cell).
+export const has_visible_symmetry_overlay = (elements, show_kinds = DEFAULT_SHOW_SYM_KINDS) => elements.some((elem) => show_kinds[elem.kind] ?? false);
+const ELEM_TOL = 1e-6;
+// The 12 edges of the unit cube [0,1]³ (corner pairs differing in exactly one coord)
+const UNIT_CUBE_EDGES = (() => {
+    const corners = [];
+    for (let x = 0; x <= 1; x++) {
+        for (let y = 0; y <= 1; y++)
+            for (let z = 0; z <= 1; z++)
+                corners.push([x, y, z]);
+    }
+    const edges = [];
+    for (let idx_a = 0; idx_a < corners.length; idx_a++) {
+        for (let idx_b = idx_a + 1; idx_b < corners.length; idx_b++) {
+            const manhattan = corners[idx_a].reduce((sum, val, dim) => sum + Math.abs(val - corners[idx_b][dim]), 0);
+            if (manhattan === 1)
+                edges.push([corners[idx_a], corners[idx_b]]);
+        }
+    }
+    return edges;
+})();
+// moyo-wasm serializes nalgebra matrices as flat 9-arrays in COLUMN-major order
+export const mat3_from_flat_col_major = (flat) => [
+    [flat[0], flat[3], flat[6]],
+    [flat[1], flat[4], flat[7]],
+    [flat[2], flat[5], flat[8]],
+];
+const mat_round = (mat) => mat.map((row) => row.map((val) => Math.round(val)));
+const mat_add = (mat_a, mat_b) => mat_a.map((row, idx) => row.map((val, jdx) => val + mat_b[idx][jdx]));
+const mat_scale = (mat, factor) => mat.map((row) => row.map((val) => val * factor));
+const mat_negate = (mat) => mat_scale(mat, -1);
+const IDENTITY = [
+    [1, 0, 0],
+    [0, 1, 0],
+    [0, 0, 1],
+];
+const is_identity = (mat) => mat.every((row, idx) => row.every((val, jdx) => val === (idx === jdx ? 1 : 0)));
+const trace = (mat) => mat[0][0] + mat[1][1] + mat[2][2];
+// Projection onto the invariant (+1 eigenvalue) subspace P = (1/n) Σₖ Wᵏ, plus the
+// matrix order n (crystallographic: 1, 2, 3, 4 or 6)
+function invariant_projector(mat) {
+    let sum = IDENTITY;
+    let power = mat;
+    for (let order = 1; order <= 6; order++) {
+        if (is_identity(power))
+            return { proj: mat_scale(sum, 1 / order), order };
+        sum = mat_add(sum, power);
+        power = mat_round(math.dot(power, mat));
+    }
+    throw new Error(`Matrix is not of finite crystallographic order`);
+}
+const gcd = (val_a, val_b) => val_b === 0 ? val_a : gcd(val_b, val_a % val_b);
+// Extract the (1D) invariant axis of a proper rotation as a reduced integer vector with
+// canonical sign (first nonzero component positive). proj must have rank 1.
+function axis_from_projector(proj, order) {
+    // n·P is an integer matrix whose nonzero columns all span the axis
+    const int_proj = mat_round(mat_scale(proj, order));
+    let best = null;
+    let best_norm = 0;
+    for (let col = 0; col < 3; col++) {
+        const vec = [int_proj[0][col], int_proj[1][col], int_proj[2][col]];
+        const norm = Math.abs(vec[0]) + Math.abs(vec[1]) + Math.abs(vec[2]);
+        if (norm > best_norm) {
+            best = vec;
+            best_norm = norm;
+        }
+    }
+    if (!best)
+        return null;
+    const divisor = best.reduce((acc, val) => gcd(acc, Math.abs(val)), 0);
+    let axis = best.map((val) => val / divisor);
+    const first_nonzero = axis.find((val) => val !== 0) ?? 1;
+    // normalize -0 to 0 when flipping to canonical sign (first nonzero positive)
+    if (first_nonzero < 0)
+        axis = axis.map((val) => (val === 0 ? 0 : -val));
+    return axis;
+}
+// Fixed point of the affine map x ↦ W·x + w_loc as the orbit average of the origin.
+// Exact whenever w_loc has no component in the invariant subspace (P·w_loc = 0).
+function fixed_point(mat, w_loc, order) {
+    let current = [0, 0, 0];
+    const sum = [0, 0, 0];
+    for (let iter = 0; iter < order; iter++) {
+        if (iter > 0)
+            current = math.add(math.mat3x3_vec3_multiply(mat, current), w_loc);
+        sum[0] += current[0];
+        sum[1] += current[1];
+        sum[2] += current[2];
+    }
+    return sum.map((val) => val / order);
+}
+// NOTE on epsilon: 1e-8 is the loosest of three intentionally different wrap
+// helpers (vs wrap_frac_coord @1e-10 [[src/lib/structure/pbc.ts:26]] for parsed
+// coords and wrap_frac @1e-9 [[src/lib/symmetry/index.ts:80]] for standardized
+// Wyckoff positions). Inputs here are fixed points / intercepts obtained by
+// solving linear systems and averaging over operation order, so float error is
+// largest; the result feeds toFixed()-based dedup keys for symmetry elements,
+// which need both near-0 and near-1 snapped onto exactly 0 to stay stable near
+// cell boundaries. Do not unify: tightening this epsilon breaks element dedup.
+const wrap_point = (pos) => pos.map((coord) => {
+    const wrapped = coord - Math.floor(coord); // always in [0, 1)
+    // snap near-0 and near-1 (which wraps to near-0) onto exactly 0
+    return wrapped < 1e-8 || wrapped > 1 - 1e-8 ? 0 : wrapped;
+});
+// Enumerate lattice translations invariant under W (lying along the axis / in the
+// plane), including centering vectors of non-primitive cells (I/F/A/B/C/R): without
+// them, e.g. the body-centering (1/2,1/2,1/2) period along ⟨111⟩ axes is missed and
+// centering-composed mirrors get mislabeled as glides. Candidates r + c with
+// r ∈ {-1,0,1}³ cover all cases for moyo translations, which lie in [0,1)³.
+function invariant_translations(mat, centerings) {
+    const result = [];
+    for (let dx = -1; dx <= 1; dx++) {
+        for (let dy = -1; dy <= 1; dy++) {
+            for (let dz = -1; dz <= 1; dz++) {
+                for (const centering of [[0, 0, 0], ...centerings]) {
+                    const cand = [dx + centering[0], dy + centering[1], dz + centering[2]];
+                    if (cand.every((val) => Math.abs(val) < ELEM_TOL))
+                        continue;
+                    const mapped = math.mat3x3_vec3_multiply(mat, cand);
+                    if (mapped.some((val, idx) => Math.abs(val - cand[idx]) > ELEM_TOL))
+                        continue;
+                    result.push(cand);
+                }
+            }
+        }
+    }
+    return result;
+}
+// Reduce an intrinsic (in-plane glide) translation modulo invariant lattice translations
+function reduce_intrinsic_translation(w_intrinsic, candidates) {
+    let best = w_intrinsic;
+    let best_sq = math.dot(w_intrinsic, w_intrinsic);
+    for (const cand of candidates) {
+        const reduced = math.subtract(w_intrinsic, cand);
+        const sq = math.dot(reduced, reduced);
+        if (sq < best_sq - ELEM_TOL) {
+            best = reduced;
+            best_sq = sq;
+        }
+    }
+    return best;
+}
+const is_zero_vec = (vec) => vec.every((val) => Math.abs(val) < ELEM_TOL);
+// Glide letter from the reduced glide vector: a/b/c (half along one cell axis),
+// n (half along a face/body diagonal), d (quarter diagonal), g otherwise
+function glide_letter(glide_vec) {
+    const doubled = glide_vec.map((val) => val * 2);
+    const is_int = (vals) => vals.every((val) => Math.abs(val - Math.round(val)) < 1e-4);
+    if (is_int(doubled)) {
+        const nonzero = doubled.map((val) => Math.round(val)).filter((val) => val !== 0);
+        if (nonzero.length === 1)
+            return [`a`, `b`, `c`][doubled.findIndex((val) => Math.round(val) !== 0)];
+        return `n`;
+    }
+    if (is_int(glide_vec.map((val) => val * 4)))
+        return `d`;
+    return `g`;
+}
+// Translation-independent analysis of a rotation matrix. Returns null for the identity
+// (pure translations define no geometric element).
+function build_rotation_info(rotation, centerings) {
+    const mat = mat_round(mat3_from_flat_col_major(rotation));
+    const det = Math.round(math.det_3x3(mat));
+    const tr = Math.round(trace(mat));
+    if (det === 1 && tr === 3)
+        return null; // identity or pure translation
+    const { proj, order: mat_order } = invariant_projector(mat);
+    if (det === -1 && tr === -3) {
+        return {
+            mat,
+            proj,
+            mat_order,
+            kind: `inversion`,
+            order: 1,
+            axis: null,
+            axis_sq: 0,
+            period: 1,
+            invariant_candidates: [],
+        };
+    }
+    if (det === 1) {
+        // proper rotation (order from trace: −1→2, 0→3, 1→4, 2→6)
+        const proper_order_by_trace = { [-1]: 2, 0: 3, 1: 4, 2: 6 };
+        const order = proper_order_by_trace[tr];
+        if (!order)
+            throw new Error(`Invalid proper rotation trace ${tr}`);
+        const axis = axis_from_projector(proj, mat_order);
+        if (!axis)
+            throw new Error(`Failed to extract rotation axis`);
+        // shortest lattice period along the axis (1 for primitive lattices; can be 1/2 via
+        // centering vectors, e.g. (1/2,1/2,1/2) along ⟨111⟩ in body-centered cells)
+        const axis_sq = math.dot(axis, axis);
+        let period = 1;
+        for (const cand of invariant_translations(mat, centerings)) {
+            const lambda_cand = math.dot(cand, axis) / axis_sq;
+            // candidate must be parallel to the axis and shorter than the current period
+            const is_parallel = cand.every((val, idx) => Math.abs(val - lambda_cand * axis[idx]) < ELEM_TOL);
+            if (is_parallel && lambda_cand > ELEM_TOL && lambda_cand < period) {
+                period = lambda_cand;
+            }
+        }
+        return {
+            mat,
+            proj,
+            mat_order,
+            kind: `proper`,
+            order,
+            axis,
+            axis_sq,
+            period,
+            invariant_candidates: [],
+        };
+    }
+    // Improper: mirror/glide (trace 1) or rotoinversion −3/−4/−6. The proper part −W is a
+    // rotation about the same axis (the plane normal for mirrors).
+    const proper_part = mat_negate(mat);
+    const { proj: proper_proj, order: proper_order } = invariant_projector(proper_part);
+    const axis = axis_from_projector(proper_proj, proper_order);
+    if (!axis)
+        throw new Error(`Failed to extract improper-operation axis`);
+    if (tr === 1) {
+        return {
+            mat,
+            proj,
+            mat_order,
+            kind: `mirror`,
+            order: 2,
+            axis,
+            axis_sq: math.dot(axis, axis),
+            period: 1,
+            invariant_candidates: invariant_translations(mat, centerings),
+        };
+    }
+    const rotoinv_order_by_trace = { 0: 3, [-1]: 4, [-2]: 6 };
+    const order = rotoinv_order_by_trace[tr];
+    if (!order)
+        throw new Error(`Invalid improper rotation trace ${tr}`);
+    return {
+        mat,
+        proj,
+        mat_order,
+        kind: `rotoinversion`,
+        order,
+        axis,
+        axis_sq: math.dot(axis, axis),
+        period: 1,
+        invariant_candidates: [],
+    };
+}
+// Classify the operation (info.mat, w) given precomputed rotation-dependent data
+function classify_with_rotation_info(info, w) {
+    const { mat, proj, mat_order, kind, order, axis } = info;
+    const w_intrinsic = math.mat3x3_vec3_multiply(proj, w);
+    const w_loc = math.subtract(w, w_intrinsic);
+    const point = wrap_point(fixed_point(mat, w_loc, mat_order));
+    if (kind === `inversion`) {
+        return { kind, order: 1, label: `-1`, axis: null, point, translation: null };
+    }
+    if (kind === `proper`) {
+        // Screw component: w_i = λ·axis, reduced modulo the lattice period along the axis
+        const { axis_sq, period } = info;
+        const lambda_raw = math.dot(w_intrinsic, axis) / axis_sq;
+        let lambda = lambda_raw - period * Math.floor(lambda_raw / period + ELEM_TOL);
+        if (Math.abs(lambda) < ELEM_TOL)
+            lambda = 0;
+        const is_screw = lambda > ELEM_TOL;
+        const screw_part = Math.round((order * lambda) / period) % order;
+        return {
+            kind: is_screw ? `screw` : `rotation`,
+            order,
+            label: is_screw ? `${order}_${screw_part}` : `${order}`,
+            axis,
+            point,
+            translation: is_screw ? axis.map((val) => val * lambda) : null,
+        };
+    }
+    if (kind === `mirror`) {
+        const glide_vec = reduce_intrinsic_translation(w_intrinsic, info.invariant_candidates);
+        const is_glide = !is_zero_vec(glide_vec);
+        return {
+            kind: is_glide ? `glide` : `mirror`,
+            order: 2,
+            label: is_glide ? glide_letter(glide_vec) : `m`,
+            axis,
+            point,
+            translation: is_glide ? glide_vec : null,
+        };
+    }
+    // Rotoinversion −3/−4/−6 (no intrinsic translation: P = 0, so w_i = 0)
+    return { kind, order, label: `-${order}`, axis, point, translation: null };
+}
+// Classify a single operation (rotation as flat column-major 9-array, translation
+// vector, both fractional). Returns null for the identity and pure (centering)
+// translations, which define no geometric element. For non-primitive (centered) cells,
+// pass the centering vectors so intrinsic screw/glide translations are reduced modulo
+// the TRUE lattice — e.g. along a ⟨111⟩ axis of a body-centered cell the lattice period
+// is (1/2)(1,1,1), and a C-centering-composed mirror is still a mirror, not an n-glide.
+export function classify_symmetry_op(rotation, translation, centerings = []) {
+    const info = build_rotation_info(rotation, centerings);
+    return info ? classify_with_rotation_info(info, translation) : null;
+}
+// Canonical dedup key for the geometric locus of an element. Elements are identified
+// modulo lattice translations:
+// - inversion centers: the wrapped center
+// - planes: (normal, offset s = x₀·normal mod 1) — lattice translations change s by an
+//   integer since the normal is an integer vector
+// - axis lines: (direction, line intercept x₀ − λ·u wrapped mod 1) — wrapping merges
+//   lattice-equivalent parallel lines
+function element_locus_key(elem) {
+    const fmt = (val) => (Math.abs(val) < 1e-4 ? 0 : val).toFixed(4);
+    if (elem.axis === null)
+        return `center|${elem.point.map(fmt).join(`,`)}`;
+    const axis_key = elem.axis.join(`,`);
+    if (elem.kind === `mirror` || elem.kind === `glide`) {
+        const offset = math.dot(elem.point, elem.axis);
+        const wrapped = offset - Math.floor(offset + 1e-6);
+        return `plane|${axis_key}|${fmt(wrapped >= 1 - 1e-4 ? 0 : wrapped)}`;
+    }
+    const lambda = math.dot(elem.point, elem.axis) / math.dot(elem.axis, elem.axis);
+    const intercept = wrap_point(math.subtract(elem.point, elem.axis.map((val) => val * lambda)));
+    return `line|${axis_key}|${intercept.map(fmt).join(`,`)}`;
+}
+// Derive all distinct symmetry elements (modulo lattice translations) from a list of
+// space-group operations. Each operation is classified, then re-anchored with the 8
+// lattice offsets t ∈ {0,1}³ to enumerate the distinct in-cell instances of its element
+// family (e.g. the inversion centers of P-1 sit at all 8 half-lattice points; 2-fold
+// axes recur at quarter positions). Elements sharing the same geometric locus but
+// different symbols (e.g. a 2-fold axis inside a 4-fold axis) are kept as separate
+// entries — filter by `order`/`label` downstream if desired.
+export function symmetry_elements_from_ops(operations) {
+    // Centering vectors are the pure-translation operations (identity rotation, w ∉ ℤ³).
+    // They define the true lattice for screw/glide reduction in centered cells.
+    // Deduplicated since supercell inputs repeat sublattice translations.
+    const centering_keys = new Set();
+    const centerings = [];
+    for (const { rotation, translation } of operations) {
+        if (!is_identity(mat_round(mat3_from_flat_col_major(rotation))))
+            continue;
+        const wrapped = wrap_point(translation);
+        if (is_zero_vec(wrapped))
+            continue;
+        const key = wrapped.map((val) => val.toFixed(6)).join(`,`);
+        if (centering_keys.has(key))
+            continue;
+        centering_keys.add(key);
+        centerings.push(wrapped);
+    }
+    // Cache rotation-dependent analysis: supercell inputs can have thousands of ops but
+    // share at most 48 distinct rotation matrices
+    const info_cache = new Map();
+    const seen = new Map();
+    for (const { rotation, translation } of operations) {
+        const rot_key = rotation.join(`,`);
+        let info = info_cache.get(rot_key);
+        if (info === undefined) {
+            info = build_rotation_info(rotation, centerings);
+            info_cache.set(rot_key, info);
+        }
+        if (info === null)
+            continue; // identity / pure translation
+        for (let dx = 0; dx <= 1; dx++) {
+            for (let dy = 0; dy <= 1; dy++) {
+                for (let dz = 0; dz <= 1; dz++) {
+                    const shifted = [translation[0] + dx, translation[1] + dy, translation[2] + dz];
+                    const elem = classify_with_rotation_info(info, shifted);
+                    const key = `${elem.kind}|${elem.label}|${element_locus_key(elem)}`;
+                    if (!seen.has(key))
+                        seen.set(key, elem);
+                }
+            }
+        }
+    }
+    // Stable order: by kind (SYM_ELEM_KINDS sequence), then descending order, label, point
+    return [...seen.values()].sort((el1, el2) => SYM_ELEM_KINDS.indexOf(el1.kind) - SYM_ELEM_KINDS.indexOf(el2.kind) ||
+        el2.order - el1.order ||
+        el1.label.localeCompare(el2.label) ||
+        el1.point.join(`,`).localeCompare(el2.point.join(`,`)));
+}
+// Evenly-spaced dash layout along a segment of given length (Å): returns dash centers
+// (distance from the segment start) and lengths. Dashes touch both segment ends so
+// dashed axes still visually span the full cell; the gap stretches as needed. Used to
+// render screw axes dashed (vs solid pure rotations) — translation-carrying elements
+// are dashed, echoing the ITA plane-group convention.
+export function dash_segments(length, dash, gap) {
+    if (!(length > 0) || !(dash > 0) || gap < 0)
+        return [];
+    if (length <= dash)
+        return [{ center: length / 2, length }];
+    const count = Math.floor((length + gap) / (dash + gap));
+    if (count <= 1)
+        return [{ center: length / 2, length: dash }];
+    // count·dash + (count−1)·gap_actual = length, with gap_actual ≥ gap by construction
+    const gap_actual = (length - count * dash) / (count - 1);
+    return Array.from({ length: count }, (_, idx) => ({
+        center: idx * (dash + gap_actual) + dash / 2,
+        length: dash,
+    }));
+}
+// Convert a fractional direction or point to Cartesian coordinates (lattice rows are
+// basis vectors). Valid for axis directions AND plane normals (eigenvectors of the
+// fractional operator map to eigenvectors of the orthogonal Cartesian operator).
+export const frac_to_cart_direction = (frac, lattice) => math.create_frac_to_cart(lattice)(frac);
+// Clip the line (point + t·direction, fractional) to the unit cell [0,1]³ using the
+// slab method, returning the Cartesian segment endpoints (or null if the line misses
+// the cell). Used to draw rotation/screw axes spanning the rendered cell.
+export function clip_line_to_cell(point, direction, lattice, eps = 1e-9) {
+    let t_min = -Infinity;
+    let t_max = Infinity;
+    for (let dim = 0; dim < 3; dim++) {
+        if (Math.abs(direction[dim]) < eps) {
+            if (point[dim] < -eps || point[dim] > 1 + eps)
+                return null; // parallel, outside slab
+            continue;
+        }
+        const t_0 = (0 - point[dim]) / direction[dim];
+        const t_1 = (1 - point[dim]) / direction[dim];
+        t_min = Math.max(t_min, Math.min(t_0, t_1));
+        t_max = Math.min(t_max, Math.max(t_0, t_1));
+    }
+    if (t_min >= t_max - eps || !Number.isFinite(t_min) || !Number.isFinite(t_max)) {
+        return null;
+    }
+    const endpoint = (t_param) => frac_to_cart_direction(point.map((coord, idx) => coord + t_param * direction[idx]), lattice);
+    return [endpoint(t_min), endpoint(t_max)];
+}
+// Clip the plane through `point` with fractional-direct-space normal `normal_frac` to
+// the unit cell, returning the Cartesian polygon vertices in winding order (empty if
+// the plane misses the cell). The plane equation in fractional coordinates uses the
+// pullback n_eq[i] = lattice[i]·N_cart of the Cartesian normal, which is exact for
+// arbitrary (non-orthogonal) cells.
+export function clip_plane_to_cell(point, normal_frac, lattice) {
+    const normal_cart = frac_to_cart_direction(normal_frac, lattice);
+    const n_eq = [
+        math.dot(lattice[0], normal_cart),
+        math.dot(lattice[1], normal_cart),
+        math.dot(lattice[2], normal_cart),
+    ];
+    const signed_dist = (frac) => n_eq[0] * (frac[0] - point[0]) +
+        n_eq[1] * (frac[1] - point[1]) +
+        n_eq[2] * (frac[2] - point[2]);
+    const frac_points = [];
+    const tol = 1e-7;
+    // Intersect the plane with the 12 unit-cube edges (corners on the plane included)
+    for (const [edge_a, edge_b] of UNIT_CUBE_EDGES) {
+        const dist_a = signed_dist(edge_a);
+        const dist_b = signed_dist(edge_b);
+        if (Math.abs(dist_a) < tol)
+            frac_points.push(edge_a);
+        if (Math.abs(dist_b) < tol)
+            frac_points.push(edge_b);
+        if (dist_a * dist_b < -tol * tol) {
+            const frac_t = dist_a / (dist_a - dist_b);
+            frac_points.push(edge_a.map((val, dim) => val + frac_t * (edge_b[dim] - val)));
+        }
+    }
+    // Dedup and convert to Cartesian
+    const seen = new Set();
+    const cart_points = [];
+    for (const frac of frac_points) {
+        const key = frac.map((val) => val.toFixed(6)).join(`,`);
+        if (seen.has(key))
+            continue;
+        seen.add(key);
+        cart_points.push(frac_to_cart_direction(frac, lattice));
+    }
+    if (cart_points.length < 3)
+        return [];
+    // Order vertices by angle around the centroid within the plane
+    const centroid = cart_points
+        .reduce((acc, vert) => math.add(acc, vert), [0, 0, 0])
+        .map((val) => val / cart_points.length);
+    const normal_unit = math.normalize_vec(normal_cart);
+    const ref_vec = math.normalize_vec(math.subtract(cart_points[0], centroid));
+    const cross_ref = math.cross_3d(normal_unit, ref_vec);
+    return cart_points
+        .map((vert) => {
+        const rel = math.subtract(vert, centroid);
+        return { vert, angle: Math.atan2(math.dot(rel, cross_ref), math.dot(rel, ref_vec)) };
+    })
+        .sort((pt_a, pt_b) => pt_a.angle - pt_b.angle)
+        .map(({ vert }) => vert);
+}

package/dist/symmetry/wyckoff-db.d.ts

@@ -0,0 +1,9 @@
+import type { MoyoHallSymbolEntry, MoyoWyckoffPosition } from '@spglib/moyo-wasm';
+import type { WyckoffPos } from './index';
+export declare function spacegroup_wyckoff_positions(hall_number: number): MoyoWyckoffPosition[];
+export declare function spacegroup_settings(spacegroup_number: number): MoyoHallSymbolEntry[];
+export declare const wyckoff_letter: (wyckoff: string) => string;
+export declare const count_free_params: (coordinates: string) => number;
+export declare function enrich_wyckoff_rows(rows: WyckoffPos[], db_positions: MoyoWyckoffPosition[]): WyckoffPos[];
+export declare function wyckoff_sequence(rows: WyckoffPos[]): string;
+export declare function count_structure_free_params(rows: WyckoffPos[]): number | null;

package/dist/symmetry/wyckoff-db.js

@@ -0,0 +1,87 @@
+// Helpers around moyo's space-group database functions (new in moyo-wasm 0.11):
+// - wyckoff_positions(hall_number): ALL Wyckoff positions of a space-group setting
+//   (multiplicity, letter, site symmetry, representative coordinate triplet)
+// - hall_symbol_entries_from_number(number): all settings (origin choices, unique
+//   axes, cell choices) of an ITA space group
+// Plus pure helpers to join that database against the occupied Wyckoff orbits of an
+// analyzed structure (Wyckoff sequence, internal degrees of freedom, ITA coords).
+import { superscript_digits } from '../labels';
+import { hall_symbol_entries_from_number, wyckoff_positions } from '@spglib/moyo-wasm';
+// All Wyckoff positions of the space-group setting given by hall_number (1-530),
+// ordered general-position-first. moyo returns [] for out-of-range hall numbers.
+// Returns [] when the moyo WASM module is not initialized (SSR, unit tests) — callers
+// treat the database as an optional enrichment, never a hard requirement.
+export function spacegroup_wyckoff_positions(hall_number) {
+    try {
+        return wyckoff_positions(hall_number);
+    }
+    catch {
+        return [];
+    }
+}
+// All Hall-symbol entries (settings) of the ITA space group `spacegroup_number`
+// (1-230), ordered by Hall number. Returns [] when the WASM module is not initialized.
+export function spacegroup_settings(spacegroup_number) {
+    try {
+        return hall_symbol_entries_from_number(spacegroup_number);
+    }
+    catch {
+        return [];
+    }
+}
+// Wyckoff letter from a `4a`-style multiplicity+letter label. Uppercase `A` is moyo's
+// encoding of ITA's 27th letter alpha (general position of Pmmm-like groups).
+export const wyckoff_letter = (wyckoff) => /[a-zA-Z]+$/.exec(wyckoff)?.[0] ?? ``;
+// Number of free coordinate parameters in an ITA representative triplet: distinct
+// x/y/z variables, e.g. `x,y,z` → 3, `1/4,1/4,z` → 1, `x,2x,1/2` → 1, `x,-x,z` → 2
+export const count_free_params = (coordinates) => new Set(coordinates.match(/[xyz]/g)).size;
+// Attach the space-group database entry (ITA representative coordinates, site-symmetry
+// fallback) to each occupied Wyckoff row, matched by letter. Rows whose letter has no
+// database entry (or an empty database) pass through unchanged.
+export function enrich_wyckoff_rows(rows, db_positions) {
+    if (db_positions.length === 0)
+        return rows;
+    const db_by_letter = new Map(db_positions.map((pos) => [pos.letter, pos]));
+    return rows.map((row) => {
+        const entry = db_by_letter.get(wyckoff_letter(row.wyckoff));
+        if (!entry)
+            return row;
+        return {
+            ...row,
+            coordinates: entry.coordinates,
+            site_symmetry: row.site_symmetry ?? entry.site_symmetry,
+        };
+    });
+}
+// Rank `A` (ITA's alpha, the letter AFTER z) above all lowercase letters
+const letter_rank = (letter) => letter.charCodeAt(0) + (letter < `a` ? 64 : 0);
+// Wyckoff sequence of the occupied orbits: letters in descending alphabetical order
+// (general position first, ICSD convention), each with a superscript count when more
+// than one orbit occupies that letter — e.g. cubic perovskite (Pm-3m): `c b a`.
+export function wyckoff_sequence(rows) {
+    const counts = new Map();
+    for (const row of rows) {
+        const letter = wyckoff_letter(row.wyckoff);
+        if (letter)
+            counts.set(letter, (counts.get(letter) ?? 0) + 1);
+    }
+    return [...counts.entries()]
+        .sort(([letter_1], [letter_2]) => letter_rank(letter_2) - letter_rank(letter_1))
+        .map(([letter, count]) => count > 1 ? `${letter}${superscript_digits(String(count))}` : letter)
+        .join(` `);
+}
+// Internal degrees of freedom of the structure: free fractional coordinates summed
+// over occupied Wyckoff orbits. Requires every row to carry ITA coordinates (see
+// enrich_wyckoff_rows); returns null for empty rows or when any row lacks coordinates
+// so callers can hide the stat instead of showing a wrong number.
+export function count_structure_free_params(rows) {
+    if (rows.length === 0)
+        return null;
+    let total = 0;
+    for (const row of rows) {
+        if (row.coordinates === undefined)
+            return null;
+        total += count_free_params(row.coordinates);
+    }
+    return total;
+}

package/dist/table/HeatmapTable.svelte

@@ -1,6 +1,7 @@
 <script lang="ts">
   import { luminance, watch_dark_mode } from '../colors'
   import Icon from '../Icon.svelte'
+  import { download } from '../io/fetch'
   import { format_num } from '../labels'
   import { SettingsSection } from '../layout'
   import ContextMenu from '../overlays/ContextMenu.svelte'
@@ -769,7 +770,7 @@
     const row_id = get_row_id(row)
     const idx = selected_rows.findIndex((selected_row) => get_row_id(selected_row) === row_id)
     if (idx !== -1) {
-      selected_rows = selected_rows.filter((_, i) => i !== idx)
+      selected_rows = selected_rows.filter((_, row_idx) => row_idx !== idx)
     } else {
       selected_rows = [...selected_rows, row]
     }
@@ -823,7 +824,7 @@
   }
 
   function export_csv(filename = `table-export`) {
-    download_file(serialize_table(`,`, true), `${filename}.csv`, `text/csv`)
+    download(serialize_table(`,`, true), `${filename}.csv`, `text/csv`)
   }
 
   function export_json(filename = `table-export`) {
@@ -838,25 +839,13 @@
       }
       return clean_row
     })
-    download_file(
+    download(
       JSON.stringify(rows, null, 2),
       `${filename}.json`,
       `application/json`,
     )
   }
 
-  function download_file(content: string, filename: string, mime_type: string) {
-    const blob = new Blob([content], { type: mime_type })
-    const url = URL.createObjectURL(blob)
-    const link = document.createElement(`a`)
-    link.href = url
-    link.download = filename
-    document.body.append(link)
-    link.click()
-    document.body.removeChild(link)
-    URL.revokeObjectURL(url)
-  }
-
   function copy_to_clipboard() {
     navigator.clipboard.writeText(serialize_table(`\t`))
   }

package/dist/table/HeatmapTable.svelte.d.ts

@@ -44,6 +44,6 @@ type $$ComponentProps = HTMLAttributes<HTMLDivElement> & {
     }]>;
     footer?: Snippet;
 };
-declare const HeatmapTable: import("svelte").Component<$$ComponentProps, {}, "sort" | "data" | "show_controls" | "controls_open" | "show_heatmap" | "column_order" | "selected_rows" | "hidden_columns" | "loading" | "heatmap_opacity">;
+declare const HeatmapTable: import("svelte").Component<$$ComponentProps, {}, "sort" | "data" | "show_controls" | "controls_open" | "loading" | "show_heatmap" | "column_order" | "selected_rows" | "hidden_columns" | "heatmap_opacity">;
 type HeatmapTable = ReturnType<typeof HeatmapTable>;
 export default HeatmapTable;